MolNFT v1 · #158375 · protein
Crystal structure of lysyl-tRNA synthetase from chlamydia trachomatis complexed with L-lysine and cladosporin
6NS0 · Lysine--tRNA ligase: “Crystal structure of lysyl-tRNA synthetase from chlamydia trachomatis complexed with L-lysine and cladosporin”. X-ray diffraction, 4 ligands (LYS, KRS, NA), 11 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 6NS0
- Type
- protein
- Length
- 1,034 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine--tRNA ligase
- EC
- 6.1.1.6
- UniProt
- B0BAN6
- Ligands
- LYS, KRS, NA, CL
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 517 | 37% helix, 26% strand | B0BAN6 |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains A, B
- KRS · cladosporin · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 34 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.85 | 0.86 | 144 | EDO |
| 2 | 903 | 0.80 | 0.82 | 102 | LYS, KRS, PG4, EDO |
| 3 | 832 | 0.77 | 0.81 | 78 | LYS, KRS, PG4, EDO |
| 4 | 56 | 0.69 | 0.96 | 24 | empty |
| 5 | 156 | 0.67 | 0.88 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 4585 Ų buried · 64 hydrogen bonds · protein-protein
Compared structures
- 6NS0 · Crystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- B0BAN6 · AlphaFold monomer V2.0 prediction for lysine--tRNA ligase (B0BAN6) · a predicted model of the same protein · chain B against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt B0BAN6
- Elsewhere: RCSB PDB 6NS0 · PDBe 6NS0 · UniProt B0BAN6
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